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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgttctccgccgccggagtaccttttttttcttcttacagctttcgtttctcagatataacagcttgagcgttttgatctctaacaatttctgtggtttcttctattggtggatgaaaaacagCCTCAGGGAGATTACATAGATTTGCACAGGAAGAGGAATGGATATCGCCTCGACCACTTCGAGAGAAAGCGCAAGAAGGAGGCGCGTGAAGTTCACAAGC

Basic information

species Arabidopsis thaliana
transcript AT5G06360.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G06360.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA10G00490.1 (Glycine max), 3'ss of exon 1
gtacgttctccgccgccggagtaccttttttttcttcttacagctttcgtttctcagatataacagcttgagcgttttgatctctaacaatttctgtggtttcttctattggtggatgaaaaacagCCTCAGGGAGATTACATAGATTTGCACAGGAAGAGGAATGGATATCGCCTCGACCACTTCGAGAGAAAGCGCAAGAAGGAGGCGCGTGAAGTTCACAAGC
|| || ||| |  |  ||    |  |     | |||    || | ||| |      || ||      |||  | |||| ||   ||  | ||  | || | |  ||   || ||  | ||   ||||| || || |||||||||||    ||||| |      |||| || || ||||| ||||||||| | ||||||||||| ||||||||| |||||||||| |
gttcgctcttcaacttcg----atttcgcactcctttggtcaaccttctt------gacat------ttgttcttttttattattatta-ttcttatgttgttgtcgtgtgttgtgt-aattgcagCCGCAAGGGGATTACATAGAGCGTCACAGAAGAGACTATGGCTACCGTCTCGATCACTTCGAGCGGAAGCGCAAGAAAGAGGCGCGTCAAGTTCACAAAC

upper sequence: AT5G06360.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA02G35500.1 (Glycine max), 3'ss of exon 1
gtacgttctccgccgccggagtaccttttttttcttcttacagctttcgtttctcagatataacagcttgagcgttttgatctctaacaatttctgtggtttcttctattggtggatgaaaaacagCCTCAGGGAGATTACATAGATTTGCACAGGAAGAGGAATGGATATCGCCTCGACCACTTCGAGAGAAAGCGCAAGAAGGAGGCGCGTGAAGTTCACAAGC
|| || ||| |  |  ||         |||    ||| |   | ||    |||| | | ||     ||||    ||||  ||| |      || ||| |||  |    |  || |   ||    |||| || || |||||||||||    ||||| |      |||| || || ||||| ||||||||| | ||||||||||| ||||| ||| ||||||||||||
gttcgctcttcagcttcga--------tttcgcattcctttggtttaaccttcttaaacatttgttcttg----tttttttctttggtt-cttatgttgttgttgtcgtgtgtcgtgtaattgtagCCGCAAGGGGATTACATAGAACGCCACAGAAGAGACTATGGCTACCGTCTCGATCACTTCGAGCGTAAGCGCAAGAAAGAGGCACGTCAAGTTCACAAGC

upper sequence: AT5G06360.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA10G10000.1 (Glycine max), 3'ss of exon 1
gtacgttctccgccgccggagtaccttttttttcttcttacagctttcgtttctcagatataacagcttgagcgttttgatctctaacaatttctgtggtttcttctattggtggatgaaaaacagCCTCAGGGAGATTACATAGATTTGCACAGGAAGAGGAATGGATATCGCCTCGACCACTTCGAGAGAAAGCGCAAGAAGGAGGCGCGTGAAGTTCACAAGC
                         |   | |||  |||  |  |  |  |  |  | |  ||||   | | | ||||  | |       ||  | || | |  |||  || ||  | ||   ||||| || || |||||||||||    ||||| |      |||| || || || || ||||||||| | ||||||||||| ||||||||| |||||||||| |
-----------------------gttcgctcttcaacttcgatttcgcactcttttggttcaacattcttaacatttttttttt----ggttcttatgttgttgtcttctgttgtgt-aattgcagCCGCAAGGGGATTACATAGAGCGTCACAGAAGAGACTATGGCTACCGTCTTGATCACTTCGAGCGGAAGCGCAAGAAAGAGGCGCGTCAAGTTCACAAAC

upper sequence: AT5G06360.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv08s0105g00280.t01 (Vitis vinifera), 3'ss of exon 1
gtacgttctccgccgccggagtaccttttttttcttcttacagctttcgtttctcagatataacagcttgagcgttt-tgatctctaacaat-ttctgtggtttcttctattggtggatgaaaaacagCCTCAGGGAGATTACATAGATTTGCACAGGAAGAGGAATGGATATCGCCTCGACCACTTCGAGAGAAAGCGCAAGAAGGAGGCGCGTGAAGTTCACAAGC
                   |||| |  ||| ||        |  ||||   |   |||| ||    |   |  ||   |||| ||| |   | || |||||||  || |||||     ||     ||||| || ||||||||||||||  | || |||||| |  |||| |||||||  ||||| |||||| | ||||||||||| ||||| ||||||||||||||||
----------------gttagtatccgtttgtttccaaggaaaatttc-cctagaagatttatttccaacaaagtcagtgatttctgattgtattttgtggttgtttgtattgtcctctgttt--cagCCGCAAGGAGATTACATAGACCTTCATAGGAAGCGCCATGGCTATCGCCCTGACCATTTCGAGCGCAAGCGCAAGAAAGAGGCTCGTGAAGTTCACAAGC

upper sequence: AT5G06360.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: EFJ37687 (Selaginella moellendorffii), 3'ss of exon 1
gtacgttctccgccgccggagtaccttttttttcttcttacagctttcgtttctcagatataacagcttgagcgttttgatctctaacaatttctgtggtttcttctattggtggatgaaaaacagCCTCAGGGAGATTACATAGATTTGCACAGGAAGAGGAATGGATATCGCCTCGACCACTTCGAGAGAAAGCGCAAGAAGGAGGCGCGTGAAGTTCACAAGC
                                                          ||      ||||  || ||||   |||  ||    |   | |      | || ||    |  |  |||||||||||||||||||| ||||||||| | ||| || |||| || ||||  ||  ||||||| || || ||||||||||| || || || || |||||||
---------------------------------------------------------gtaagcgctcttgctcgatttg-cttcttgcagcagcccagctgatagattttcgtctgcgccat-cagCCTCAGGGAGATTACATCGATTTGCACCGCAAGCGGCATGGGTACCGCCCGGATTACTTCGAAAGGAAACGCAAGAAGGATGCTCGGGAGGTCCACAAGC

upper sequence: AT5G06360.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: EFJ15002 (Selaginella moellendorffii), 3'ss of exon 1
gtacgttctccgccgccggagtaccttttttttcttcttacagctttcgtttctcagatataacagcttgagcgttttgatctctaacaatttctgtggtttcttctattggtggatgaaaaacagCCTCAGGGAGATTACATAGATTTGCACAGGAAGAGGAATGGATATCGCCTCGACCACTTCGAGAGAAAGCGCAAGAAGGAGGCGCGTGAAGTTCACAAGC
                                                          ||      ||||  || ||||   |||  ||    |   | |      | ||  |    |  |  |||||||||||||||||||| ||||||||| | ||| || |||| || ||||| ||  ||||||| || || ||||||||||| || || || || |||||||
---------------------------------------------------------gtaagcgctcttgctcgatttg-cttcttgcagcagcccagctgatagattttcatttgcgccat-cagCCTCAGGGAGATTACATCGATTTGCACCGCAAGCGGCATGGGTACCGCCTGGATTACTTCGAAAGGAAACGCAAGAAGGATGCTCGGGAGGTCCACAAGC

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|86050590|gb|DR346345.1|DR346345
EST:     CGTCTCTCTCTCTTTTTATCTCACCGTCTGATCGCTTAGAAGCAACCATA                         CCTCAGGGAGATTACATAGATTTGCACAGGAAGAGGAATGGATATCGCCTC
genomic: CGTCTCTCTCTCTTTTTATCTCACCGTCTGATCGCTTAGAAGCAACCATGgtacgttctc ... tgaaaaacagCCTCAGGGAGATTACATAGATTTGCACAGGAAGAGGAATGGATATCGCCTC
EST: gi|86050587|gb|DR346342.1|DR346342
EST:     CGTCTCTCTCTCTTTTTATCTCACCGTCTGATCGCTTAGAAGCAACCATA                         CCTCAGGGAGATTACATAGATTTGCACAGGAAGAGGAATGGATATCGCCTC
genomic: CGTCTCTCTCTCTTTTTATCTCACCGTCTGATCGCTTAGAAGCAACCATGgtacgttctc ... tgaaaaacagCCTCAGGGAGATTACATAGATTTGCACAGGAAGAGGAATGGATATCGCCTC
EST: gi|86050592|gb|DR346347.1|DR346347
EST:     CGTCTCTCTCTCTTTTTATCTCACCGTCTGATCGCTTAGAAGCAACCATG                         CCTCAGGGAGATTACATAGATTTGCACAGGAAGAGGAATGGATATCGCCTC
genomic: CGTCTCTCTCTCTTTTTATCTCACCGTCTGATCGCTTAGAAGCAACCATGgtacgttctc ... tgaaaaacagCCTCAGGGAGATTACATAGATTTGCACAGGAAGAGGAATGGATATCGCCTC
EST: gi|86050595|gb|DR346350.1|DR346350
EST:     CGTCTCTCTCTCTTTTTATCTCACCGTCTGATCGCTTAGAAGCAACCATG                         CCTCAGGGAGATTACATAGATTTGCACAGGAAGAGGAATGGATATCGCCTC
genomic: CGTCTCTCTCTCTTTTTATCTCACCGTCTGATCGCTTAGAAGCAACCATGgtacgttctc ... tgaaaaacagCCTCAGGGAGATTACATAGATTTGCACAGGAAGAGGAATGGATATCGCCTC
EST: gi|163971873|gb|ES148989.1|ES148989
EST:     CTGATCGCTTAGAAGCAACCATG                         CCTCAGGGGGATTACATAGATTTGCACAGGAAGAGGAA
genomic: CTGATCGCTTAGAAGCAACCATGgtacgttctc ... tgaaaaacagCCTCAGGGAGATTACATAGATTTGCACAGGAAGAGGAA
EST: gi|86050588|gb|DR346343.1|DR346343
EST:     GATCGCTTAGAAGCAACCATG                         CCTCAGGGAGATTACATAGATTTGCACAGGAAGAGGAATGGATATCGCCTC
genomic: GATCGCTTAGAAGCAACCATGgtacgttctc ... tgaaaaacagCCTCAGGGAGATTACATAGATTTGCACAGGAAGAGGAATGGATATCGCCTC
EST: gi|116396688|gb|EG439280.1|EG439280
EST:     CCGTCTGATCGCTTAGAAGCAACCATG                         CCTCAGGGAGATTACATAGATTTGCACAGGAAGAGGAATGGATATCGCCTC
genomic: CCGTCTGATCGCTTAGAAGCAACCATGgtacgttctc ... tgaaaaacagCCTCAGGGAGATTACATAGATTTGCACAGGAAGAGGAATGGATATCGCCTC
EST: gi|86050586|gb|DR346341.1|DR346341
EST:     CGTCTCTCTCTCTTTTTATCTCACCGTCTGATCGCTTAGAAGCAACCATG                         CCTCAGGGAGATTACATAGATTTGCACAGGAAGAGGAATGGATATCGCCTC
genomic: CGTCTCTCTCTCTTTTTATCTCACCGTCTGATCGCTTAGAAGCAACCATGgtacgttctc ... tgaaaaacagCCTCAGGGAGATTACATAGATTTGCACAGGAAGAGGAATGGATATCGCCTC
EST: gi|86050591|gb|DR346346.1|DR346346
EST:     CGTCTCTCTCTCTTTTTATCTCACCGTCTGATCGCTTAGAAGCAACCATG                         CCTCAGGGAGATTACATAGATTTGCACAGGAAGAGGAATGGATATCGCCTC
genomic: CGTCTCTCTCTCTTTTTATCTCACCGTCTGATCGCTTAGAAGCAACCATGgtacgttctc ... tgaaaaacagCCTCAGGGAGATTACATAGATTTGCACAGGAAGAGGAATGGATATCGCCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcgttttgatctctaacaatttctgtggtttcttctattggtggatgaaaaacagCCTCAGGGAGATTACATAGATTTGCACAGGAAGAGGAATGGATATCGCCTCGACCACTTCGAGAGAAAGCGCAAGAAGGAGGCGCGTGAAGTTCACAAGC
          ctctaac  putative branch site (score: 2)
             taacaattt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgttctccgccgccggagtaccttttttttcttcttacagctttcgtttctcagatataacagcttgagcgttttgatctctaacaatttctgtggtttcttctattggtggatgaaaaacagCCTCAGGGAGATTACATAGATTTGCACAGGAAGAGGAATGGATATCGCCTCGACCACTTCGAGAGAAAGCGCAAGAAGGAGGCGCGTGAAGTTCACAAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG